X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FCutAndPasteTransfer.java;h=f3c4d87a985e94ecd79ce6fd9276a643a3e1e4e5;hb=refs%2Fheads%2Ffeatures%2FJAL-653_gffalignments;hp=5465d33ae2ab389b4a6d9c792290b979fda41ff4;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 5465d33..f3c4d87 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -1,31 +1,50 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
 
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+
+import jalview.api.ComplexAlignFile;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.io.FileParse;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GCutAndPasteTransfer;
+import jalview.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
 
 /**
@@ -39,6 +58,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
   AlignViewport viewport;
 
+  FileParse source = null;
   public CutAndPasteTransfer()
   {
     SwingUtilities.invokeLater(new Runnable()
@@ -98,7 +118,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
     chooser.setAcceptAllFileFilterUsed(false);
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle("Save Text to File");
+    chooser.setDialogTitle(MessageManager.getString("label.save_text_to_file"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
     int value = chooser.showSaveDialog(this);
@@ -174,35 +194,61 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     {
       try
       {
-        al = new FormatAdapter().readFile(getText(), "Paste", format);
+        FormatAdapter fa = new FormatAdapter(viewport);
+        al = fa.readFile(getText(), "Paste", format);
+        source = fa.getAlignFile();
+
       } catch (java.io.IOException ex)
       {
         JOptionPane.showInternalMessageDialog(Desktop.desktop,
-        		MessageManager.formatMessage("label.couldnt_read_pasted_text", new String[]{ex.toString()}),
-                MessageManager.getString("label.error_parsing_text"), JOptionPane.WARNING_MESSAGE);
+                MessageManager.formatMessage(
+                        "label.couldnt_read_pasted_text", new String[]
+                        { ex.toString() }), MessageManager
+                        .getString("label.error_parsing_text"),
+                JOptionPane.WARNING_MESSAGE);
       }
     }
 
     if (al != null)
     {
+      String title = MessageManager.formatMessage(
+              "label.input_cut_paste_params", new String[]
+              { format });
       if (viewport != null)
       {
-        for (int i = 0; i < al.getHeight(); i++)
-        {
-          viewport.getAlignment().addSequence(al.getSequenceAt(i));
-        }
-
-        viewport.firePropertyChange("alignment", null, viewport
-                .getAlignment().getSequences());
+        viewport.addAlignment(al, title);
       }
       else
       {
-        AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
-                AlignFrame.DEFAULT_HEIGHT);
+
+        AlignFrame af;
+        if (source instanceof ComplexAlignFile)
+        {
+          ColumnSelection colSel = ((ComplexAlignFile) source)
+                  .getColumnSelection();
+          SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+                  .getHiddenSequences();
+          boolean showSeqFeatures = ((ComplexAlignFile) source)
+                  .isShowSeqFeatures();
+          ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+          af = new AlignFrame(al, hiddenSeqs, colSel,
+                  AlignFrame.DEFAULT_WIDTH,
+                  AlignFrame.DEFAULT_HEIGHT);
+
+          af.getViewport().setShowSequenceFeatures(showSeqFeatures);
+          af.changeColour(cs);
+        }
+        else
+        {
+          af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+                  AlignFrame.DEFAULT_HEIGHT);
+        }
+
         af.currentFileFormat = format;
-        Desktop.addInternalFrame(af, MessageManager.formatMessage("label.input_cut_paste_params", new String[]{format}),
-                AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
-        af.statusBar.setText(MessageManager.getString("label.successfully_pasted_alignment_file"));
+        Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
+                AlignFrame.DEFAULT_HEIGHT);
+        af.statusBar.setText(MessageManager
+                .getString("label.successfully_pasted_alignment_file"));
 
         try
         {
@@ -215,6 +261,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     }
   }
 
+
   /**
    * DOCUMENT ME!
    * 
@@ -235,8 +282,10 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
   {
     if (SwingUtilities.isRightMouseButton(e))
     {
-      JPopupMenu popup = new JPopupMenu(MessageManager.getString("action.edit"));
-      JMenuItem item = new JMenuItem(MessageManager.getString("action.copy"));
+      JPopupMenu popup = new JPopupMenu(
+              MessageManager.getString("action.edit"));
+      JMenuItem item = new JMenuItem(
+              MessageManager.getString("action.copy"));
       item.addActionListener(new ActionListener()
       {
         public void actionPerformed(ActionEvent e)